BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927068.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 22,695,710 number of mapped reads = 22,011,093 (96.98%) number of supplementary alignments = 572,322 (2.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 11,051,881 number of mapped paired reads (second in pair) = 10,959,212 number of mapped paired reads (both in pair) = 21,604,908 number of mapped paired reads (singletons) = 406,185 number of mapped bases = 1,988,352,689 bp number of sequenced bases = 1,986,921,810 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,768,522 duplication rate = 6.32% >>>>>>> Insert size mean insert size = 287,890.7296 std insert size = 5,242,805.2604 median insert size = 180 >>>>>>> Mapping quality mean mapping quality = 52.7817 >>>>>>> ACTG content number of A's = 569,669,856 bp (28.67%) number of C's = 383,652,671 bp (19.31%) number of T's = 581,480,346 bp (29.27%) number of G's = 451,851,581 bp (22.74%) number of N's = 267,356 bp (0.01%) GC percentage = 42.05% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 20,479,370 number of insertions = 330,306 mapped reads with insertion percentage = 1.47% number of deletions = 972,246 mapped reads with deletion percentage = 4.31% homopolymer indels = 51.55% >>>>>>> Coverage mean coverageData = 0.6423X std coverageData = 2.551X There is a 31.06% of reference with a coverageData >= 1X There is a 14.9% of reference with a coverageData >= 2X There is a 7.36% of reference with a coverageData >= 3X There is a 3.98% of reference with a coverageData >= 4X There is a 2.25% of reference with a coverageData >= 5X There is a 1.32% of reference with a coverageData >= 6X There is a 0.81% of reference with a coverageData >= 7X There is a 0.51% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.1% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.06% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.03% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 164404783 0.6595962824100647 3.8989466003364255 chr2 243199373 175974887 0.723582815322472 4.184197450772651 chr3 198022430 139773671 0.7058476708926358 1.40334884322437 chr4 191154276 125199253 0.6549644382530057 2.1946809306771167 chr5 180915260 123921539 0.6849700738345676 1.365553508913644 chr6 171115067 112537874 0.6576736693794475 1.4178735626875445 chr7 159138663 105399979 0.6623153482193074 2.0489129801889656 chr8 146364022 98409813 0.672363410456157 1.630873337900528 chr9 141213431 87222059 0.6176612124097459 2.7765711609058124 chr10 135534747 98174094 0.724346310986953 4.723318445160403 chr11 135006516 90381651 0.6694613984409463 1.9056957958694563 chr12 133851895 89294652 0.6671153366935896 1.3613632866646606 chr13 115169878 58764835 0.5102448315522223 1.1640102061581632 chr14 107349540 60386036 0.5625178831693177 1.3073962665130139 chr15 102531392 54158587 0.528214685703282 1.217891074933639 chr16 90354753 61737671 0.6832808341582207 3.4364034956399605 chr17 81195210 50590519 0.623072703426717 2.0591025336072746 chr18 78077248 51095244 0.6544191209198357 2.9189678330953193 chr19 59128983 31398124 0.5310107227787091 2.2194151271722986 chr20 63025520 43619048 0.6920854917182754 1.4872079392142787 chr21 48129895 25290555 0.5254645787197333 1.7402769086816943 chr22 51304566 22319301 0.4350353728749991 1.1932158784105784 chrMT 16571 126484 7.63285257377346 4.199496593698232 chrX 155270560 113349418 0.7300122959561683 1.6428332999180597 chrY 59373566 4822612 0.08122490065696913 2.982297748885432